Interview: Functional consequences of gut microbiome and resistome dynamics

This is the seventh interview with the PhD students of the Complex Systems & Metagenomics projects in a series of background articles. Keep following this website for the next interview in this series.


Interview with Paul Stege, PhD student of the project ‘Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) and enterococci’ at the Department of Medical Microbiology University Medical Center Utrecht.

‘During my bachelor I started learning how bacteria play a role in our environment, but also in our bodies. I was amazed to learn that bacteria are present in such large numbers and with high diversity, thereby forming complex ecosystems. Nevertheless, we know little about the microbial interactions that take place and how this affects us.’

‘Due the increasing appearance of antibiotic resistant bacteria, I became interested in studying the transmission routes of pathogens and their genes from environmental sources to humans. I now study potential transmission routes, such as transfer from person to person in households, zoonotic or food based transmission. I specifically focus on the transmission of antibiotic resistant genes. These genes are often located on mobile genetic elements that can easily be transmitted both vertically to daughter cells, but also horizontally to other species. By unravelling transmission routes, I hope to ultimately reduce the amount of outbreaks of some major recurring antibiotic resistant pathogens.’

‘In one of my projects I compare groups of healthy people with contrasting diets to determine diet based differences in both the intestinal microbiota and the reservoir of resistance genes that it harbours; the resistome. Results are still pending, but preliminary data indicates that both the intestinal microbiota as the resistome can show profiles correlating with a particular diet. In a similar way I study transmission of pathogens and their genes between dogs and their owners. What makes these studies interesting for me, is that novel sequencing techniques are used to zoom to such a level of detail, that I will identify pathogens and genes that previously would have gone undetected, whilst still posing a threat.’

‘In addition to the in vivo studies I work with a new organoid model that in many ways closely resembles human intestinal cells and can reveal host-pathogen interactions. These organoids can help unravel the mechanisms by which some pathogens are able to colonize the human intestinal microbiota and subsequently causing infection. Applying organoids in this way has proven to be challenging, although initial results confirm the relevance of this model and continues to fascinate me.’

PhD project: Molecular mechanisms of microbiota-mediated colonization resistance against intestinal outgrowth of multidrug-resistant Enterobacteriaceae (E. coli, K. pneumoniae) and enterococci.

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